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L. Paavolainen · SciRah

Researcher profile · Semantic Scholar

L. Paavolainen

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L. Paavolainen — researcher profile on SciRah

h-index: 20
Works: 85
Citations: 2,500

Most-cited papers

Data-analysis strategies for image-based cell profiling
J. Caicedo, S. Cooper, F. Heigwer, S. Warchal +20 more
2017Nature Methods729 citations Open access
Semantic Scholar
BioImageXD: an open, general-purpose and high-throughput image-processing platform
P. Kankaanpää, L. Paavolainen, Silja Tiitta, M. Karjalainen +5 more
2012Nature Methods224 citations
Semantic Scholar
nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin A. Tasnádi +21 more
2020Cell Systems217 citations Open access
Semantic Scholar
Association of tamoxifen resistance and lipid reprogramming in breast cancer
S. Hultsch, M. Kankainen, L. Paavolainen, Ruusu-Maaria Kovanen +4 more
2018BMC Cancer157 citations Open access
Semantic Scholar
Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis
Sami Blom, L. Paavolainen, Dmitrii Bychkov, Riku Turkki +6 more
2017Scientific Reports152 citations Open access
Semantic Scholar
Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer.
K. Saeed, V. Rahkama, S. Eldfors, D. Bychkov +13 more
2017European Urology92 citations Open access
Semantic Scholar
Intelligent image-based in situ single-cell isolation
C. Braskó, Kevin Smith, C. Molnar, N. Faragó +14 more
2018Nature Communications83 citations Open access
Semantic Scholar
Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.
F. Piccinini, Tamás Balassa, Ábel Szkalisity, C. Molnar +8 more
2017Cell Systems79 citations Open access
Semantic Scholar
Nucleus segmentation: towards automated solutions.
Réka Hollandi, Nikita Moshkov, L. Paavolainen, Ervin A. Tasnádi +2 more
2022Trends in Cell Biology76 citations Open access
Semantic Scholar
ADC measurements in diffuse large B-cell lymphoma and follicular lymphoma: a DWI and cellularity study.
Xing-Chen Wu, H. Pertovaara, P. Dastidar, M. Vornanen +5 more
2013European Journal of Radiology73 citations
Semantic Scholar
Fibroblast subsets in non-small cell lung cancer: associations with survival, mutations, and immune features.
T. Pellinen, L. Paavolainen, A. Martín-Bernabé, Renata Papatella Araujo +14 more
2022Journal of the National Cancer Institute69 citations Open access
Semantic Scholar
A functional genetic screen defines the AKT-induced senescence signaling network
K. Chan, S. Blake, Hao-Ran Zhu, Jian Kang +11 more
2019Cell Death and Differentiation65 citations Open access
Semantic Scholar
A deep learning framework for nucleus segmentation using image style transfer
Réka Hollandi, Ábel Szkalisity, Tímea Tóth, Ervin A. Tasnádi +20 more
2019bioRxiv48 citations Open access
Semantic Scholar
UNC-45a promotes myosin folding and stress fiber assembly
Jaakko I. Lehtimäki, Aidan M. Fenix, T. Kotila, Giuseppe Balistreri +4 more
2017Journal of Cell Biology45 citations Open access
Semantic Scholar
N- and O-methylation of sphingomyelin markedly affects its membrane properties and interactions with cholesterol.
Anders Björkbom, T. Róg, P. Kankaanpää, Daniel Lindroos +11 more
2011Biochimica et Biophysica Acta43 citations Open access
Semantic Scholar
Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography
L. Paavolainen, Erman Acar, U. Tuna, S. Peltonen +5 more
2014PLoS ONE36 citations Open access
Semantic Scholar
Spatial immunoprofiling of the intratumoral and peritumoral tissue of renal cell carcinoma patients
O. Brück, Moon H. Lee, Riku Turkki, Ilona Uski +8 more
2021Modern Pathology30 citations Open access
Semantic Scholar
BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows
Ulysse Rubens, Romain Mormont, L. Paavolainen, Volker Bäcker +14 more
2020Patterns29 citations Open access
Semantic Scholar
Calpains promote α2β1 integrin turnover in nonrecycling integrin pathway
Nina Rintanen, M. Karjalainen, J. Alanko, L. Paavolainen +8 more
2012Molecular Biology of the Cell29 citations Open access
Semantic Scholar
Automatic detection and analysis of cell motility in phase‐contrast time‐lapse images using a combination of maximally stable extremal regions and Kalman filter approaches
M. Kaakinen, S. Huttunen, L. Paavolainen, V. Marjomäki +2 more
2014Journal of Microscopy22 citations
Semantic Scholar
A functional genetic screen defines the AKT-induced senescence signaling network
K. Chan, S. Blake, Hao-Ran Zhu, Jian Kang +11 more
2019Cell Death and Differentiation19 citations Open access
Semantic Scholar
Trimeric HIV Env provides epitope occlusion mediated by hypervariable loops
C. G. Moscoso, L. Xing, Jin-Wen Hui, Jeffrey Hu +10 more
2014Scientific Reports14 citations Open access
Semantic Scholar
Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT).
Michaela Feodoroff, P. Mikkonen, L. Turunen, A. Hassinen +6 more
2023SLAS discovery : advancing life sciences R & D13 citations Open access
Semantic Scholar
Ellagitannin-rich cloudberry inhibits hepatocyte growth factor induced cell migration and phosphatidylinositol 3-kinase/AKT activation in colon carcinoma cells and tumors in Min mice
A. Pajari, E. Päivärinta, L. Paavolainen, E. Vaara +6 more
2016OncoTarget13 citations Open access
Semantic Scholar
Application independent greedy particle tracking method for 3D fluorescence microscopy image series
L. Paavolainen, P. Kankaanpää, P. Ruusuvuori, G. McNerney +2 more
2012IEEE International Symposium on Biomedical Imaging13 citations
Semantic Scholar
Regression plane concept for analysing continuous cellular processes with machine learning
Ábel Szkalisity, F. Piccinini, A. Beleon, Tamás Balassa +13 more
2021Nature Communications10 citations Open access
Semantic Scholar
Combining High-Content Imaging and Phenotypic Classification Analysis of Senescence-Associated Beta-Galactosidase Staining to Identify Regulators of Oncogene-Induced Senescence
K. Chan, L. Paavolainen, K. Hannan, Amee J. George +4 more
2016Assay and drug development technologies9 citations
Semantic Scholar
Multiparametric platform for profiling lipid trafficking in human leukocytes
Simon G. Pfisterer, I. Brock, K. Kanerva, I. Hlushchenko +12 more
2022Cell Reports Methods8 citations Open access
Semantic Scholar
Permeability Changes of Integrin-Containing Multivesicular Structures Triggered by Picornavirus Entry
P. Soonsawad, L. Paavolainen, Paula Upla, Wattana Weerachatyanukul +5 more
2014PLoS ONE8 citations Open access
Semantic Scholar
Prognostic Role of Tumor Immune Microenvironment in Pleural Epithelioid Mesothelioma
Hely Ollila, M. Mäyränpää, L. Paavolainen, J. Paajanen +8 more
2022Frontiers in Oncology7 citations Open access
Semantic Scholar
Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome.
Mariia S. Bogacheva, S. Kuivanen, S. Potdar, Antti Hassinen +15 more
2024Antiviral Research6 citations Open access
Semantic Scholar
Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2
V. Pietiäinen, Minttu Polso, E. Migh, C. Guckelsberger +28 more
2023Cell Reports Methods6 citations Open access
Semantic Scholar
Quantitative Analysis of Dynamic Association in Live Biological Fluorescent Samples
P. Ruusuvuori, L. Paavolainen, K. Rutanen, Anita Mäki +2 more
2014PLoS ONE6 citations Open access
Semantic Scholar
ROR1-PI3K/AKT signaling drives adaptive resistance to cell cycle blockade in TP53 mutated ovarian cancer
Juuli Raivola, Frida Rantanen, Alice Dini, Emilia Piki +8 more
2026Cell Death and Disease5 citations Open access
Semantic Scholar
Evaluating feature extraction in ovarian cancer cell line co-cultures using deep neural networks
Osheen Sharma, Greta Gudoityte, Rezan Minozada, Olli Kallioniemi +3 more
2025Communications Biology5 citations Open access
Semantic Scholar
EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020)
M. Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones +34 more
20205 citations Open access
Semantic Scholar
Tumor cell FAP orchestrates EMT and immune suppression in aggressive localized ccRCC
T. Pellinen, L. Luomala, K. Mattila, A. Hemmes +13 more
2026Theranostics4 citations Open access
Semantic Scholar
Multi-scale modeling of human tissues from spatial transcriptomics with TERRA
Sebastian Birk, M. V. Sanian, Amirhossein Vahidi, S. Ogden +53 more
2026bioRxiv4 citations Open access
Semantic Scholar
Piximi - An Images to Discovery web tool for bioimages and beyond
Levin M Moser, Nodar Gogoberidze, A. Papaleo, Alice M. Lucas +14 more
2024bioRxiv4 citations Open access
Semantic Scholar
Regression plane concept: analysing continuous cellular processes with machine learning
Ábel Szkalisity, F. Piccinini, A. Beleon, Tamás Balassa +11 more
2020bioRxiv4 citations Open access
Semantic Scholar
EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update)
M. Kalaš, Laure Plantard, Natasa Sladoje, Joakim Lindblad +22 more
20194 citations Open access
Semantic Scholar
Echovirus 1 internalization negatively regulates epidermal growth factor receptor downregulation
Moona Huttunen, Paula Turkki, Anita Mäki, L. Paavolainen +2 more
2017Cellular Microbiology4 citations Open access
Semantic Scholar
Fibroblast Activation Protein Defines an Aggressive, Immunosuppressive EMT-associated Tumor Subtype in Highly Inflamed Localized Clear Cell Renal Cell Carcinoma
T. Pellinen, L. Luomala, K. Mattila, A. Hemmes +12 more
2025bioRxiv3 citations Open access
Semantic Scholar
CHAMMI-75: pre-training multi-channel models with heterogeneous microscopy images
Vidit Agrawal, John Peters, Tyler N. Thompson, M. V. Sanian +12 more
2025arXiv.org3 citations
Semantic Scholar
Functional screening identifies kinesin spindle protein inhibitor filanesib as a potential treatment option for hepatoblastoma
Ruth Nousiainen, K. Eloranta, J. Saarela, Antti Hassinen +11 more
2025npj Precision Oncology3 citations Open access
Semantic Scholar
Artificial intelligence aided serum protein electrophoresis analysis of Finnish patient samples: Retrospective validation.
T. Lahtiharju, L. Paavolainen, J. Suvisaari, Pasi Nokelainen +3 more
2024Clinica chimica acta; international journal of clinical chemistry3 citations Open access
Semantic Scholar
BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows
Ulysse Rubens, Romain Mormont, Volker Baecker, Gino Michiels +15 more
2019bioRxiv3 citations Open access
Semantic Scholar
Fibroblast activation protein defines aggressive EMT-associated cancer cell state and prognosis in localized ccRCC
T. Pellinen, L. Luomala, K. Mattila, A. Hemmes +12 more
3 citations
Semantic Scholar
Self-supervised learning enables unbiased patient characterization from multiplexed cancer tissue microscopy images
Gantugs Atarsaikhan, Isabel Mogollon, Katja Välimäki, T. Mirtti +2 more
2025bioRxiv2 citations Open access
Semantic Scholar
3D-Guided Scalable Flow Matching for Generating Volumetric Tissue Spatial Transcriptomics from Serial Histology
M. V. Sanian, Arshia Hemmat, Amirhossein Vahidi, Jonas Maaskola +8 more
2025arXiv.org2 citations
Semantic Scholar

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